[R-sig-Debian] Update to 2.8 and problem with liblapack

[Dirk Eddelbuettel]

On 15 November 2008 at 12:36, Matthieu Stigler wrote:
| Hello
| 
| To update from R 2.6 to 2.8 (on Ubuntu 8.04 both) I had to install new 
| tcl and liblapack packages (excuse me it is in french):
          ^^^^^^^^^

| >  sudo apt-get install r-base-dev
| > Lecture des listes de paquets... Fait
| > Construction de l'arbre des dépendances       
| > Lecture des informations d'état... Fait
| > Les paquets supplémentaires suivants seront installés :
| >   libblas-dev liblapack-dev r-base-core tcl8.5 tk8.5
| > Paquets suggérés :
| >   cdbs
| > Les paquets suivants seront ENLEVÉS :
| >   refblas3-dev
| > Les NOUVEAUX paquets suivants seront installés :
| >   libblas-dev liblapack-dev tcl8.5 tk8.5
| > Les paquets suivants seront mis à jour :
| >   r-base-core r-base-dev
| > 2 mis à jour, 4 nouvellement installés, 1 à enlever et 19 non mis à jour.
| It installed libblas-dev liblapack-dev and removed refblas3-dev.
| 
| I'm now unable to run the Matrix library, whatever I install it from 
| within R or with apt-get, it claims a problem:
| 
| > library(Matrix)
| > Loading required package: lattice
| > Error in dyn.load(file, DLLpath = DLLpath, ...) :
| >   unable to load shared library '/usr/lib/R/site-library/Matrix/libs/Matrix.so':
| >   libRlapack.so: cannot open shared object file: No such file or
      ^^^^^^^^^^^^^
| > directory

| > Error: package/namespace load failed for 'Matrix'
| 
| but there is a file Natrix.so in this directory (but no libRlapack.so)
| 
| Do you see where the problem is? Was I right to update R in this manner?

Short story: You did nothing wrong, but you now need to update / reinstall
your matrix package as it is a user of lapack.

The long story is that Debian finally switched from an older to a newer atlas
/ lapack which allowed us to change how R uses lapack. It uses to be internal
(hence libRlapack.so indicating R's sources for lapack function), it is now
using the system-wide package.  So for that you need to install the matching
Matrix package (ie 'sudo apt-get install r-cran-matrix) or rebuild one
yourself.

Hth, Dirk

-- 
Three out of two people have difficulties with fractions.